A python package to determine the location and the size of telomeric repeats (both terminal and internal) from genome assemblies.
Telomere detection is based on calculation in a 20 bp sliding window of the following two metrics:
- DNA sequence entropy < entropy_threshold (default=0.8)
- proportion of polynucleotides (default_list = ["CC", "CA", "AC"]) > polynuc_threshold (default=0.8)
The complete documentation is available at Read The Docs
telofinder fasta_path_to_file(s)
telofinder.py --help
Telofinder outputs a directory called telofinder_results including 3 csv and 2 bed files containing the telomere calls and their coordinates, either as raw output or after merging consecutive calls
Please cite O’Donnell, S., Yue, JX., Saada, O.A. et al. Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae. Nat Genet 55, 1390–1399 (2023). DOI